Representation of base frequencies along 663 nt of Rhodophyta COI. Nucleotide frequency values (G, C, A, and T from top to bottom row) for a given site are reported on a red to blue scale (0 to 100% conservation). The positions of GazR1  and our nested primer, R686, are displayed and the GC-rich region in which R686 lies is highlighted. The numerous polyTs in COI 3'end (four or more successive thymidines), potentially affecting GazR1 specificity, can be seen as thick blue bands. The multiple alignment used to create this figure contained accessions EF136591-EF434941, Z47547 NC_001677 and AF118119 (Gigartinales and Gracilariales), Z48930, D89861 and NC_000887 (Cyanidiales), and AF114794 and NC_002007 (Bangiales), which were selected for their length, extending past GazR1. The region shown depicts sites 205-868 of the Cyanidium caldarium (Z48930) complete COI sequence.
Sherwood et al. BMC Plant Biology 2010 10:258 doi:10.1186/1471-2229-10-258